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Yorodumi- PDB-6mkw: Crystal structure of the periplasmic Lysine-, Arginine-, Ornithin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mkw | |||||||||||||||
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Title | Crystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) D11A mutant from Salmonella typhimurium complexed with histidine | |||||||||||||||
Components | Lysine/arginine/ornithine transport protein | |||||||||||||||
Keywords | PROTEIN BINDING / Periplasmic Binding Protein / LAO / Thermodynamics / Protein Ligand Complex | |||||||||||||||
Function / homology | Function and homology information amino acid transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space Similarity search - Function | |||||||||||||||
Biological species | Salmonella typhimurium (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.32 Å | |||||||||||||||
Authors | Romero-Romero, S. / Vergara, R. / Espinoza-Perez, G. / Rodriguez-Romero, A. | |||||||||||||||
Funding support | Mexico, 4items
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Citation | Journal: Febs J. / Year: 2020 Title: The interplay of protein-ligand and water-mediated interactions shape affinity and selectivity in the LAO binding protein. Authors: Vergara, R. / Romero-Romero, S. / Velazquez-Lopez, I. / Espinoza-Perez, G. / Rodriguez-Hernandez, A. / Pulido, N.O. / Sosa-Peinado, A. / Rodriguez-Romero, A. / Fernandez-Velasco, D.A. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mkw.cif.gz | 63.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mkw.ent.gz | 44.5 KB | Display | PDB format |
PDBx/mmJSON format | 6mkw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6mkw_validation.pdf.gz | 440.3 KB | Display | wwPDB validaton report |
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Full document | 6mkw_full_validation.pdf.gz | 442 KB | Display | |
Data in XML | 6mkw_validation.xml.gz | 12 KB | Display | |
Data in CIF | 6mkw_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/6mkw ftp://data.pdbj.org/pub/pdb/validation_reports/mk/6mkw | HTTPS FTP |
-Related structure data
Related structure data | 6mkuC 6mkxC 6ml0C 6ml9C 6mlaC 6mldC 6mleC 6mlgC 6mliC 6mljC 6mlnC 6mloC 6mlpC 6mlvC 1lagS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25943.225 Da / Num. of mol.: 1 / Mutation: D11A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (strain 14028s / SGSC 2262) (bacteria) Strain: 14028s / SGSC 2262 / Gene: argT, STM14_2901 / Plasmid: pET12b / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): AI / References: UniProt: A0A0F6B499, UniProt: P02911*PLUS | ||
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#2: Chemical | ChemComp-HIS / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.23 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M Sodium acetate trihydrate 0.1 M Sodium cacodylate trihydrate 30% w/v Polyethylene glycol 8,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Apr 10, 2018 / Details: Osmic VariMax Cu-HF |
Radiation | Monochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→50 Å / Num. obs: 11213 / % possible obs: 97.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 19.2 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.098 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 2.32→2.36 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 1055 / CC1/2: 0.885 / % possible all: 93.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LAG Resolution: 2.32→35.148 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.56
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.32→35.148 Å
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Refine LS restraints |
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LS refinement shell |
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